-
Notifications
You must be signed in to change notification settings - Fork 2
/
abysscmast.swarm
executable file
·30 lines (30 loc) · 11.8 KB
/
abysscmast.swarm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
abyss-pe k=76 j=16 name=1_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=1_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=1_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/1_S1_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=2_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=2_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=2_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/2_S2_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=3_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=3_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=3_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/3_S3_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=4_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=4_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=4_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/4_S4_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=5_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=5_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=5_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/5_S5_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=6_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=6_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=6_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/6_S6_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=7_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=7_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=7_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/7_S7_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=8_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=8_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=8_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/8_S8_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=9_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=9_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=9_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/9_S9_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=76 j=16 name=10_cmastrc110 in='/data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=86 j=16 name=10_cmastrc120 in='/data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R2_001_unpaired_trimmed_2.fastq.gz'
abyss-pe k=96 j=16 name=10_cmastrc130 in='/data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R1_001_paired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R2_001_paired_trimmed_2.fastq.gz' se='/data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R1_001_unpaired_trimmed_1.fastq.gz /data/cmast/Results/Trimmomatic/trimmedfastq/10_S10_L001_R2_001_unpaired_trimmed_2.fastq.gz'